For the Virgin Australia group of airlines, there are three earning schemes - domestic (based on $ spent), international short haul and international long haul (both of the latter use fare buckets and based on distance flown). If you booked a SQ operated VA codeshare (i.e. your flight number is VA....), then you would use the international long haul earn table to determine how many points you would get.
For your example of BNE-MLE, here's an illustration of how this would work. Go to the SQ website and put in your points of travel, dates and class (Economy, in this case). Then we get the screen below.
View attachment 6624
If you were to book this ticket, you'd have two flights which are both operated and marketed by SQ (i.e. an SQ aircraft will fly you there, and the flight number on your ticket is an SQ one). I've only shown the outbound here (but it'd equally apply for the inbound flight).
To find out whether you will earn any points or not, you'll need to read the detailed fare information. To do this, scroll to the bottom of the page and click on "View summary of fare conditions". You'll get a screen which looks like this (in this case, the fare type selected is "Super Deals"):
View attachment 6625
In this case, the fare basis is
VLPR3M, corresponding to a fare bucket / class code of
V (the initial letter of the fare basis). If you then go to the Points Earn on partner tables on VFF, look under the SQ section, you'll see that V class is not found in the table. This means you will earn
nothing under VFF if you booked this fare.
On the other hand, if we select a Flexi Saver fare type, and view the detailed conditions, we get the following information instead:
View attachment 6626
In this case, the fare bucket will be
W. Under the VFF table for SQ, W is in the Economy section and you'll earn 1 VFF point per mile flown. (If you check the status earn table, you'll also find that you'll earn Full Economy status credits). When you book your SQ ticket, be sure to add your VFF number to the frequent flyer information (i.e. along with all your other passenger information). You can also try adding it at the airport if need be.